@afwang1: To be honest, I don’t know. I’m impressed that you have the discipline to do this much box stepping. Are you in an area without the terrain for hilly hikes outside?
You’re right that cycling won’t be as effective a stimulus, and it sounds like running is not ideal right now. The only suggestions that I have would be to try to improve your running by running, even if it is painfully slow. Over the long haul, I think that you’ll benefit from having more activities to choose from.
As far as the box-stepping in particular, I don’t think that it could be too much other than if it’s hard mentally. If it becomes a grind mentally, then I would change it up. It’s important to maintain your enthusiasm for training.
Training-wise, it seems like the most specific activity that you have. Changing up the height of the box may be a good idea from time to time. Typical box steps are much higher than the actual step height used hiking and climbing.
I hope that helps.